Senior Research Associate, Strain Engineering

Socket.dev; Cambridge (MA); On-site; USD 81,000 - 107,000; Full time

Job summary

Flagship Pioneering is seeking a highly motivated Senior Research Associate to support microbial strain engineering for recombinant protein production in Cambridge, MA. Reporting to the Senior Scientist, this role emphasizes hands-on genetic engineering using DNA design and assembly techniques and robust lab operations in a fast-paced startup environment.

The ideal candidate will have a strong background in molecular biology, aseptic technique, and independent experiment execution, with 3–7

Qualifications

• Bachelor’s degree with 5–7 years of relevant research in bioengineering or related field.
• Hands-on molecular biology experience in DNA design, isolation and assembly.
• Strong aseptic technique and microbial culture handling.
• Excellent communication and documentation skills.
• Ability to independently execute experiments.

Responsibilities

• Construct plasmids using modern molecular techniques (Golden Gate, HiFi, etc.).
• Perform sequencing analysis with state-of-the-art NGS tools.
• Prepare plasmid DNA via mini-preps and maxi-preps.
• Transform microbial strains by preparing competent cells.
• Run PCR to prepare substrates and genotype strains.
• Perform gel electrophoresis and nucleic acid quantification.
• Support screening of strains in shake flasks and microtiter plates.
• Track biomass, assay readouts, and product formation.
• Maintain cell banks and inventory records.
• Prepare media for strain-building campaigns.
• Maintain safety culture and meticulous documentation.
• Collaborate with discovery, bioprocess development, downstream and analytical teams.

Skills

Molecular biology

Aseptic technique

Experiment execution

Documentation

Education

Bachelor's degree in Bioengineering/related

Master's degree in Bioengineering/related

Tools

Benchling

Geneious

Job description

Company Description

Flagship Pioneering is a platform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies.

The Role

We are seeking a highly motivated Senior Research Associate to support the development and optimization of microbial strain engineering for recombinant protein production. Reporting to the Senior Scientist, Microbial Strain Engineering, this individual will play a key role in genetic engineering of microbial strains in a fast-paced startup environment.

The ideal candidate is highly hands-on, technically rigorous, and comfortable operating independently in a dynamic research setting. This role requires strong practical experience with DNA assembly strategies, microbial culture techniques, and laboratory operations.

Key Responsibilities

DNA Design and Assembly

• Construct plasmids using modern molecular biology techniques (e.g: Golden Gate assembly, HiFi assembly, etc.)
• Perform sequencing analysis using state-of-the-art NGS technologies and software
• Prepare plasmid DNA through mini-preps, maxi-preps, etc.

Strain Engineering and Evaluation

• Prepare competent cells for transformation of microbial strains
• Execute PCR to both prepare substrates for genetic engineering and genotyping of candidate strains
• Perform agarose gel electrophoresis, nucleic acid quantification, and sample preparation for routine functional assays
• Support screening and characterization of microbial strains in shake flask and microtiter plates
• Track strain performance metrics including biomass production, functional assay readouts, and product formation

Laboratory Operations

• Generate and maintain microbial cell banks and inventory records
• Prepare media for strain-building campaigns
• Support routine laboratory maintenance, equipment upkeep, and troubleshooting
• Contribute to safe laboratory operations and maintain a strong culture of safety and operational rigor
• Maintain accurate and well-organized experimental records and documentation

Cross-Functional Collaboration

• Collaborate with discovery, bioprocess development, downstream, and analytical teams to support integrated process development activities
• Closely partner with bioprocess development to align on best practices for strain development and evaluation

Professional Experience & Qualifications

• Bachelor’s degree (with 5-7 years of relevant research experience) or Master’s degree (with 3-5 years of relevant research experience) in Bioengineering, Biochemistry, Microbiology, Biotechnology, or related discipline.
• Hands-on experience in molecular biology, including design, isolation, and assembly of DNA
• Strong understanding of aseptic technique and microbial culture handling
• Strong communication, organizational and documentation skills
• Ability to independently execute experiments and troubleshoot routine process issues

Preferred Experience

• Experience engineering industrial microbial hosts such as E. coli, Bacillus, yeast, or filamentous fungal systems
• Experience with flow cytometry, protein purification, assay design and implementation
• Familiarity with Benchling and Geneious

Location

Cambridge, MA

About Flagship Pioneering

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

We are an equal opportunity employer

All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

The salary range for this role is $81,000 - $107,250. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos's good faith estimate as of the date of publication and may be modified in the future.

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